Not sure if its been said in detail but dont care to look, heres my answer.
You have to consider what each system can do to determine whether its homebrew is "better". First off 3DS brew has been around longer and has been worked on more extensively than the Vita, so thats a factor. So let me seperate it for you.
Emulators.
Yes Retroarch seems to work better on Vita so far, and the Vita is stronger so it can do more. Granted, again too early to tell. They both can do alot, and even without retroarch the 3ds can run handhelds from gba and back, as well as consoles like snes and back. Desmume is now on both for ds games, albeit still new. I believe tho that we may see an N64 emulator on the vita, and (if that guy isnt kidding) dreamcast. Still, too early to say.
Applications.
This i may go with 3ds. They both can do ftp, install custom themes (easier on 3ds tho) and run test apps. The Vita has VHBL for psp homebrew, and i believe the 3ds now can do some dsi brew. Theres save editors, but (dont quote me here) i think the 3ds is the only one who can backup saves atm.
Backups.
As it stands, you can backup 3ds and vita games, but you can only install true backups on 3ds.
System utilities
Currently you can only spoof firmware, have emunand, spoof eshop, and downgrade on 3ds. Not sure if vita has or will have that.
Cheats and mods
Afaik only on 3ds but i know theres something for Vita. Still too early for Vita but its being worked on.
I think that covers all i can think of. Its hard to really say which is better between the two right now. Give the vita another good year.
Now if you were asking about the greatest homebrew machine of all time, ill let you decide. Its either xbox, psp, or wii.